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PhD position in metabolomics and functional genomics of halogenation mechanisms in brown algae

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Monday, June 5, 2023 - 16:00
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General information:

Workplace: Roscoff Biological Station, France Publication date of the offer : 2 June 2023

Scientific supervisors: Catherine Leblanc et Soizic Prado Contract type: Doctoral contract (CDD)

Contract period: 36 months

Start date of the thesis: September/October 2023 Proportion of work: Full time

Salary: 2 135,00 € gross monthly

 

Description of the thesis project

Objectiveandsubject scientificfield andthemes.

The halogen metabolism is thought to play a unique role in the biology of macroalgae, but the biosynthetic pathways, the chemical nature and the biological roles of halogenated compounds in vivo are poorly described. The HALOGENE project is interested in the evolution and role of this metabolism in brown algae, through the study of key halogenating enzymes. These enzymes include vanadium- dependent haloperoxidases (vHPOs) which were discovered more than thirty years ago in a brown alga and form large multigenic families in this eukaryotic lineage (1). vHPOs catalyse the oxidation of halides in the presence of hydrogen peroxide to produce a reactive intermediate, which can halogenate various substrates. They could be involved in oxidative detoxification, cell wall reinforcement and the production of halogenated compounds during abiotic and biotic defence responses (2). However, the physiological substrates for vHPOs have not been identified, and their biological role has yet to be validated in brown algae.

This PhD research project aims at studying the biochemical role of vHPOs and at deciphering the biosynthetic pathways of halogenated compounds in a model brown alga, Ectocarpus siliculosus, by combining functional genomics and metabolomics approaches. A recently developed protocol for switching off the expression of target genes using the CRISPR-Cas9 method (3) has generated several knock-out (KO) mutants of the vHPO gene in Ectocarpus. By studying these mutants and by comparing them with wild-type strains, this thesis project will analyse the contribution of this enzyme to halogenation processes in this brown alga species. The first step will be to validate the loss of protein activity using crude protein extracts, and then to optimise the chemical extraction conditions and analysis methods for profiling the whole halogenated metabolome by mass spectrometry (LC-MS) (4). The metabolomic profiles of the different strains will be compared, in laboratory cultures under standard conditions or submitting to oxidative stress. Halogenated metabolites will be detected thanks to their isotopic mass using Haloseeker-type tools, annotated and characterised using molecular network-type approaches and using natural product and internal databases. Their biosynthesis will be further explored in vitro by incubating putative substrates, commercially available, with algal protein extracts. Transcriptomic analyses will also be carried out on the different strains in culture, and the combination of metabolomic and transcriptomic data will be used to decipher the main metabolic pathways linked to halogen metabolism.

 

Expected results and valorisation of the PhD student's research work

This research project will lead to original results on the chemical nature of halogenated compounds in a model brown alga and the characterisation of the biochemical functions of halogenation enzymes and of the corresponding biosynthetic pathways.

 

References.

  1. Leblanc et al. (2015) Vanadium haloperoxidases: from the discovery 30 years ago to X-Ray crystallographic and V K-edge absorption spectroscopic studies. Coordination Chemistry Reviews, 301–302, 134–146. doi.org/10.1016/j.ccr.2015.02.013
     
  2. La Barre et al. (2010) The Halogenated Metabolism of Brown Algae (Phaeophyta), Its Biological Importance and Its Environmental Significance. Marine Drugs 8(4), 988-1010. doi.org/10.3390/md8040988
     
  3. Badis et al. (2021) Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytol, 231: 2077-2091. doi.org/10.1111/nph.17525
     
  4. Roullier et al. (2016) Automated Detection of Natural Halogenated Compounds from LC-MS Profiles–Application to the Isolation of Bioactive Chlorinated Compounds from Marine-Derived Fungi. Anal. Chem. 2016, 88, 18, 9143– 9150. https://doi.org/10.1021/acs.analchem.6b02128

 

Work context

This PhD thesis will be carried out in the context of the HALOGENE project (2022-2026), funded by the French National Research Agency (ANR) and involving the 'Biology of Algae and Interactions with the Environment' (ABIE) and 'Genetics of Macroalgae' teams from the Laboratory of Integrative Biology of Marine Models (LBI2M, UMR8227, Sorbonne University-CNRS) in Roscoff and the team headed by Soizic Prado at the National Museum of Natural History (MCAM, UMR7245, CNRS-MNHN) in Paris. This thesis work will be co-directed by Catherine Leblanc (DR CNRS HDR, ABIE team) and Soizic Prado (PR MNHN HDR, MCAM). Their work is related to fundamental research and based on an interdisciplinary approach, at the interface between chemistry of natural products and macroalgal functional genomics. The candidate will carry out his or her experimental work within the ABIE team with the support of the laboratory's algal culture facility in Roscoff. The metabolomic and chemical analyses (LC- and GC-MS) will be carried out jointly on the MetaboMer platform (mass spectrometry) of the FR2424 in Roscoff and on the mass spectrometry and NMR platforms of the MNHN in Paris. He or she will take part in HALOGENE project meetings, interact with the other scientists involved in this collaborative research project and benefit from the scientific dynamism of the Roscoff Biological Station.

 

Constraints and risks

The doctoral project will be linked to the doctoral school 227, ''Sciences de la nature et de l'Homme : évolution et écologie'' of Sorbonne Université-MNHN. The candidate will be registered at Sorbonne Université, and will benefit from the dedicated environment in terms of doctoral training and support for doctoral students. He or she will work mainly in Roscoff and will carry out short-term scientific visits at the MNHN laboratory in Paris, for metabolomics analyses.

 

Additional information:

We are looking for a motivated candidate with a Master or Engineering degree in chemistry or biochemistry. Knowledge or experience in metabolomics analysis would be an advantage. Applications should include a detailed CV, at least two references (likely to be contacted), a one-page covering letter and previous Master 1-2 or engineering school grades.

Applications may only be submitted via the CNRS portal: https://emploi.cnrs.fr/Offres/Doctorant/UMR8227-SOPLAB-028/Default.aspx  Deadline for applications: 23 June 2023

Contact:

Catherine Leblanc (catherine.leblanc@sb-roscoff.fr) and Soizic Prado (soizic.prado@mnhn.fr)

Job opportunities
Laboratory of Integrative Biology of Marine Models

[Phd Defense] Reproduction in the red alga Gracilaria gracilis: demography, biotic interactions and sexual selection.

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Tuesday, June 27, 2023 - 14:30
Station Biologique de Roscoff - Salle de conférence
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 THE THESIS WILL FOCUS ON reproduction in the red alga Gracilaria gracilis: demography, biotic interactions and sexual selection. 

The jury will be composed of : 

Agnès Mignot, Professor, University of Montpellier - Rapporter

Stacy A. Krueger-Hadfield, Associate Professor, University of Alabama - Rapporter

Mathilde Dufaÿ, Professor, University of Montpellier  - Examiner     

Xavier Vekemans, Research Director, EPP, Lille - Examiner      

Julien Gasparini, Professor, Sorbonne University, Paris - Examiner     

Marie-Laure GUILLEMIN, Professor, UACH, Valdivia - Thesis supervisor

Myriam Valero,  Research Director, CNRS, Roscoff - Thesis supervisor

 

Abstract

Red algae have a sexual life cycle, involving three types of individuals: diploid tetrasporophytes and haploid male and female gametophytes. The particularities of their reproduction are that: i) the male gametes lack a flagellum, ii) the female gametes (carpogonia) are not released and iii) after fertilization the zygote develops on the female into a complex structure called a cystocarp. In the absence of a flagellum the transport of spermatia to the female gametes is largely dependent on water movement. This thesis aims to study the consequences of this reproductive cycle on the demographic functioning of a natural population using an exhaustive spatial and temporal survey in the red alga Gracilaria gracilis, as well as the evolutionary strategies implemented to enhance the gametes encounter using experimental approaches.

First, the frequency, fertility and survival of the three types of individuals monitored over time validate the predictions of the demographic models on the maintenance of the haploid-diploid cycle and on the dynamics of this population, typical of a perennial species with a generation time of several decades. Results confirm the high survival of individuals (more than half of the individuals are still present 25 years after the first surveys) and the low demographic growth of the population. This demographic and phenological survey also allowed to highlight the presence of individuals named "life cycle variants": either haploids carrying both male and female organs, or diploids carrying tetraspores and/or male and female organs or tetrasporophytes presenting epiphytic male and female gametophytes. The evolutionary consequences that these variations (observed at a frequency of 5%) could have on the maintenance of the haplo-diplophasic life cycle are discussed and constitute interesting research perspectives. Finally, this survey of a natural population revealed the presence in high frequency of an isopod (Idotea balthica) that mimics the fronds of the G. gracilis. This animal was thus selected as a candidate model to test the transport of the male gametes to the female thallus.

Secondly, an experimental approach combined with confocal microscopy observations allowed to demonstrate the existence of I. balthica-mediated fertilization in G. gracilis. This result shows, for the first time, the involvement of biotic interactions in the dispersal of gametes of a red alga (similar to pollination in plants), a group of species for which the classical dogma was that fertilizations were only due to water movements. Moreover, this result raises questions about the origin of pollination, which could be much older than the radiation of angiosperms. This work opens new avenues for future studies to verify the widespread occurrence of this animal-mediated fertilization in red algae and to further investigate the algae-animal relationship.

Finally, among the evolutionary mechanisms that influence reproduction, sexual selection has been widely studied in animals but only rarely in plants and even less in algae. To test its importance in G. gracilis, the reproductive success and number of mates of male and female individuals were estimated through paternity analyses carried out in the natural population. Results showed that the opportunity for sexual selection is present in G. gracilis, a species where sexual dimorphism is absent. In plants, animal pollination has played a role in the coevolution of plants and insects and it is hypothesized that traits involved in pollinator attractiveness are more likely to be under sexual selection. Another new investigation opened by this thesis is to further explore this link between the role of animals and traits under sexual selection in Gracilaria gracilis, such as reproductive phenology or mucilage production during gamete release.

Key words : Idotea balthica - Animal-mediated fertilization in the sea - Haploid-diploid life cycle - Life cycle variations – Demographic and genetic survey – Bateman’s principles

Emma Lavaut
PhD thesis defense
Evolutionary Biology and Ecology of Algae

[PhD defense] advantage conferred by chromatic acclimation in marine cyanobacteria.

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Louison Dufour will defend her thesis on Friday 8 September at 10:00 a.m. The defence will focus on the advantage conferred by chromatic acclimatisation in marine cyanobacteria. It will take place in the Station Biologique de Roscoff's conference room and by videoconference.
Friday, September 8, 2023 - 10:00
Zoom
Station Biologique de Roscoff - Salle de conférence
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JURY

Pr. Nicole Frankenberg-Dinkel, Technische Universitat Kaiserkautern-Landau
Pr. David Scanlan, University of Warwick
Dr. Cristiana Callieri, Water Research Institute of Verbania
Pr. Stéphane Egee, Sorbonne Université - Roscoff
Dr. Frédéric Partensky, CNRS - Roscoff
Dr. Laurence Garczarek, CNRS - Roscoff

PhD thesis defense
Roscoff Marine Station
Adaptation and Diversity in the Marine Environment

[Thesis defence ] "The evolution of recombination in self-fertilising species"

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[Thesis defence ] "The evolution of recombination in self-fertilising species: theoretical approach and genomic study of linkage disequilibrium between deleterious mutations in several Angiosperm species
Monday, September 18, 2023 - 09:00
Station Biologique de Roscoff - Salle de conférence
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Document(s)

Abstract

pdf 76.62 KB

JURY

Dr. Sylvain GANDON            CNRS Montpellier                   Rapporteur
Dr. Susan JOHNSTON           University of Edinburgh        Rapporteur
Pr. Guillaume ACHAZ           Université Paris Cité              Examiner
Dr. Claire MÉROT                  CNRS Rennes                          Examiner
Dr. Denis ROZE                      CNRS Roscoff                          Thesis supervisor
Dr. Henrique TEOTÓNIO      ENS Paris                                 Invited member

Roman STETSENKO
PhD thesis defense
Evolutionary Biology and Ecology of Algae

Postdoctoral researcher in marine microbiology (M/W)

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15-months postdoc position open  to study transcriptomic regulations in macroalgae-degrading bacteria as part of the X-Reg project. 
Tuesday, November 21, 2023 - 12:00
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The job offer is available here: https://emploi.cnrs.fr/Offres/CDD/UMR8227-FRATHO-004/Default.aspx?lang=EN

Application deadline is December 11th, for an expected start date on February 1st.
Applicants should have less than two years of experience after their PhD and have spent at least 18 months outside France since May 1st, 2018 and April 1st, 2023.
 

Job opportunities
Laboratory of Integrative Biology of Marine Models

Second international conference on marine flavobacteria - 27 to 31 May 2024

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Registrations are now opened for the Second international conference on marine flavobacteria. This conference will be held at the Roscoff Biological Station (France) from 27th to 31st of May 2024.
Monday, November 27, 2023 - 10:15
Zoom
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The conference will cover a wide range of topics related to marine flavobacteria, with three sessions focusing on (1) diversity and ecology, (2) Flavobacteria/Host interactions, (3) functional genomics, biochemistry and biotechnology applications.

Information including the preliminary program with 6 exciting keynote lectures from invited speakers covering diverse fields  on  the website  : https://marine-flavobacteria-2024.colloque.inrae.fr/

The deadline for abstract submission is February 1st, 2024.

 

Event
Laboratory of Integrative Biology of Marine Models
Roscoff Marine Station

establishment of the apico-basal and medio-lateral axes in the embryogenesis of the brown alga Saccharina latissima.

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Thursday, December 21, 2023 - 09:30
Station Biologique de Roscoff - Salle de conférence
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Chikako Nagasato, Rapportrice
Muroran Marine Station (Japon)

Kenny Bogaert, Rapporteur
Max Planck Institute for Biology Tübingen (Allemagne)

Alex Mc Dougall, Examinateur
Institut de la Mer de Villefranche (France)

Philippe Andrey, Examinateur
INRAE-AgroParisTech (France)

Charlotte Kirchhelle, Examinatrice
Laboratoire Reproduction et Développement des Plantes (France)

Bénédicte Charrier, Directrice de thèse
Institut de Génomique Fonctionnelle de Lyon (France)

Samuel Boscq
PhD thesis defense
Roscoff Marine Station

"Sexual reproduction and chemical interactions in the parasite Amoebophrya ceratii infecting the dinoflagellate host Scrippsiella acuminata".

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SOUTENANCE DE THESE
Thursday, December 14, 2023 - 13:00
Station Biologique de Roscoff - Salle de conférence
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Julia Kubanek, Rapporteur
Georgia Institute of Technology, USA

Assaf Vardi, Rapporteur
Weizmann Institute of Science, Israël 

Flora Vincent, Examiner
EMBL Heidelberg, Germany

Erik Selander, Examiner 
University of Gothenburg, Sweden

Christophe Destombe, Examiner
Station Biologique de Roscoff, France

Laure Guillou, Thesis director
Station Biologique de Roscoff, France

Georg Ponhert, Thesis co-director
Friedrich Schiller University Jena – Max Planck Institute for Chemical Ecology, Germany

Marine Vallet, Thesis co-director
Friedrich Schiller University Jena – Max Planck Institute for Chemical Ecology, Germany

Chemical communication, involving the release and detection of signaling molecules, plays a crucial role in species interactions. This communication is essential for functions such as sexual attraction, territory marking, food foraging, and defense. In this thesis, we have explored this communication between a widespread yet poorly understood parasite, Amoebophrya ceratii, and its host, Scrippsiella acuminata, a dinoflagellate capable of producing colorful blooms. This parasite is an interesting model as it inevitably kills its host to complete its infectious cycle in less than two days and has a very limited host range.

This thesis first focused on studying the free-living stage of the parasite. The first chapter reveals the existence of two types of spores, one infectious and the other dedicated to sexual reproduction. We also demonstrate that an infected host cell produces a unique type of spore, and the determinism to produce one type or the other is certainly induced well before infection. The second chapter describes metabolic changes in parasites during infection, suggesting a potential host defense mechanism. The third chapter evaluates the chemotactic ability of spores, a crucial step for infection, using microfluidics.

Overall, this thesis provides new insights into the biology of this parasite, shedding light on key aspects of its biology, chemical communication, and interactions with hosts. It has generated a wealth of data that remains to be further explored, paving the way for future research to better understand sexual reproduction, chemotaxis, and other aspects of the biology of these parasites in marine plankton.

Jeremy Szymczak
PhD thesis defense
Adaptation and Diversity in the Marine Environment

"Metabolism of polysaccharides from the extracellullar matrix of brown algae: evolutionary history and proteomic analysis".

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SOUTENANCE DE THESE
Monday, December 4, 2023 - 14:00
Station Biologique de Roscoff - Salle de conférence
No
Advanced

The defence will be conducted in French in front of a jury composed of:
 

Dr Thierry Tonon , University of York, United Kingdom
Rapporteur

Pr Christophe Dunand, Université Paul Sabatier, Toulouse
Rapporteur

Dr Catherine Rayon, Université de Picardie Jules Verne, Amiens
Examiner

Pr Nathalie Bourgougnon, Université Bretagne Sud, Vannes
Examiner

Pr Christophe Destombe, Station Biologique de Roscoff, SU/CNRS, Roscoff
Examiner

Dr Cécile HERVE, Station Biologique de Roscoff, SU/CNRS, RoscoffThesis director

 

Lisa Mazéas
PhD thesis defense
Laboratory of Integrative Biology of Marine Models

[Training] Single-Cell : Transcriptomics, Spatial and Long reads (sincellTE)

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[Training] Single-Cell : Transcriptomics, Spatial and Long reads (sincellTE)
Tuesday, March 19, 2024 - 10:00
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Date : 20th October 2024 – 25th October 2024

Place : Roscoff, France

Deadline pre-registration: 7th May 2024

This one-week class focuses on the large-scale study of heterogeneity across individual cells from a genomics and transcriptomics points of view. Recent technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information.

This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD students and postdoctoral fellows in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis.

A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, long reads, artificial intelligence and FAIR access to the data/code.

Requirements : Participants must have prior experience on NGS data analysis with everyday use of R and/or Python and good knowledge of Unix command line. Before the training, participants are advised to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets. 

It is not necessary to have personal single-cell data to analyse.

 

All information and pre-registration:

https://moodle.france-bioinformatique.fr/course/view.php?id=27

Training
Roscoff Marine Station




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